Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6C

Orthogroup ID

OG0017377

Physical Location & Seq

Genomic Coordinates Forward (+)

2285766 .. 2290038

Gene Structure 4273 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6CG025000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 888 bp

ATGCCTGGACACGAAGTTGCCAACGATGACATGATGATCGATGAGTATGAACAGAAGCAAGTGAATGCTGTTCCTGATGGATTTAACTCTCAGTATCTCAAAATTTACTATGGAAAGCTCTTCCCATATGAGGAAATGTTTAAGTGGATGTCCTATGCAAATGATGGCAAGCATCCTGCACGCAACCAGTCCTACTTTGGCCGGAGAGAGTTTTCTTTCACACTGGATAATGATGTTTATCTGCGGTACAAAACTTTCAACTCCGTGTCTGAGCTTGAAAATTCTATCAAAGAGAAGTGCCCCGTCAAAATAGATATTGGGCCTGTGTACAATGTTGATGAGATCATATACCGAACTTTCACTTCTGAGCTTCGGGGAAAGTGGCAAGATAATAGACGAACCTCCAATGCAAAAGAAGACATTAATGTTGCTCGTTGGGAGCAGCTGAAACATATGCTGCAATCTGGGAAACAGAAGATGCAAGGACTGCGTAGATGTGTGGAGGAGATTGTGTTCTCTTATACCTACCCTAGACTTGACATGGAGGTTTCAAAACATATGAACCATTTATTAAAGGCACCATTCTGTGTACATCCAAAGACAGGTCGTGTTTGTGTTCCGATTGATCCCAACCGTTGTGAGGAGTTTGATCCTACTGCAGTTCCAACCCTTTCCACTCTTATTGAAGAACTTAATAATGAGGGTTTGAGAGCAGAGGCTGATAACGAACGGGATAGAACGTCACTTGGAAAATCAATAAGATTCTTCCAATCATCATTTTTGGAGCCTTTGGTAAAATCTTGCAAGGAGGAGATGATAAGTTCCTACAATGCGAAACTGCAGCAGTCGAAGTTGCAGCAGTCAAAGAACGTGCTTGCTGCAATCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0003824 GO:0003896 GO:0003899 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005658 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006269 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0030894 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0032993 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0043601 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03030 map00230 map00240 map01100 map03030

Pfam Domains

Protein Families

DNA_primase_S

Protein Analysis

295

Amino Acids

34.45

Weight (kDa)

6.62

Isoelectric Point (pI)

53.03

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_primase_S	PF01896	118 - 209	2.5e-14	DNA primase small subunit

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0017377)

Species	Orthologous Gene IDs
malus_domestica	MD06G1072700.v1.1 MD14G1127600.v1.1
pyrus_communis	pycom16g19580
rosa_chinensis	RchiOBHm_Chr6g0245391
rosa_laevigata	RLG00000008502 RLG00000036015
rosa_multiflora	Rmu_sc0009380.1_g000010 Rmu_sc0030772.1_g000001
rosa_rugosa	Rorug05G0394000
rosa_samantha	Rh6BG026300 Rh6CG025000 Rh7DG148900
rosa_wichuraiana	Rw2G021700

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	577
AciI	CCGC	1 cut(s)	244
AclWI	GGATC	2 cut(s)	620, 644
AcoI	YGGCCR	1 cut(s)	199
AcsI	RAATTY	2 cut(s)	102, 280
AfaI	GTAC	3 cut(s)	248, 329, 591
AfiI	CCNNNNNNNGG	3 cut(s)	130, 602, 640
AgsI	TTSAA	4 cut(s)	259, 278, 552, 686
AjnI	CCWGG	1 cut(s)	4
AloI	GAACNNNNNNTCC	2 cut(s)	497, 529
AluBI	AGCT	4 cut(s)	118, 274, 370, 445
AluI	AGCT	4 cut(s)	118, 274, 370, 445
AlwI	GGATC	2 cut(s)	620, 644
AlwNI	CAGNNNCTG	1 cut(s)	719
AoxI	GGCC	2 cut(s)	199, 320
ApeKI	GCWGC	5 cut(s)	442, 457, 841, 856, 878
ApoI	RAATTY	2 cut(s)	102, 280
AseI	ATTAAT	1 cut(s)	423
AspS9I	GGNCC	1 cut(s)	320
BaeGI	GKGCMC	1 cut(s)	302
BanI	GGYRCC	1 cut(s)	577
BbsI	GAAGAC	1 cut(s)	423
BbvI	GCAGC	5 cut(s)	444, 454, 853, 865, 868
BccI	CCATC	2 cut(s)	71, 158
BciT130I	CCWGG	1 cut(s)	6
BfaI	CTAG	2 cut(s)	531, 886
BfmI	CTRYAG	2 cut(s)	657, 839
BisI	GCNGC	5 cut(s)	443, 458, 842, 857, 879
BlsI	GCNGC	5 cut(s)	444, 459, 843, 858, 880
Bme1390I	CCNGG	1 cut(s)	6
BmgT120I	GGNCC	1 cut(s)	320
BmiI	GGNNCC	2 cut(s)	579, 786
BmrFI	CCNGG	1 cut(s)	6
BmsI	GCATC	2 cut(s)	181, 468
BpiI	GAAGAC	1 cut(s)	423
Bsa29I	ATCGAT	1 cut(s)	39
BsaBI	GATNNNNATC	1 cut(s)	237
BsaXI	ACNNNNNCTCC	2 cut(s)	497, 527
Bsc4I	CCNNNNNNNGG	3 cut(s)	130, 602, 640
Bse1I	ACTGG	2 cut(s)	187, 228
Bse8I	GATNNNNATC	1 cut(s)	237
BseBI	CCWGG	1 cut(s)	6
BseCI	ATCGAT	1 cut(s)	39
BseGI	GGATG	3 cut(s)	153, 172, 592
BseJI	GATNNNNATC	1 cut(s)	237
BseLI	CCNNNNNNNGG	3 cut(s)	130, 602, 640
BseMII	CTCAG	3 cut(s)	104, 261, 357
BseNI	ACTGG	2 cut(s)	187, 228
BseRI	GAGGAG	3 cut(s)	518, 656, 824
BseSI	GKGCMC	1 cut(s)	302
BseXI	GCAGC	5 cut(s)	444, 454, 853, 865, 868
BsgI	GTGCAG	1 cut(s)	162
BshFI	GGCC	2 cut(s)	201, 322
BshNI	GGYRCC	1 cut(s)	577
BshVI	ATCGAT	1 cut(s)	39
BsiSI	CCGG	1 cut(s)	202
BslI	CCNNNNNNNGG	3 cut(s)	130, 602, 640
BsmI	GAATGC	1 cut(s)	70
BsnI	GGCC	2 cut(s)	201, 322
Bsp1286I	GDGCHC	1 cut(s)	302
Bsp1407I	TGTACA	2 cut(s)	327, 589
Bsp143I	GATC	4 cut(s)	36, 342, 625, 649
BspACI	CCGC	1 cut(s)	244
BspANI	GGCC	2 cut(s)	201, 322
BspCNI	CTCAG	3 cut(s)	103, 262, 358
BspDI	ATCGAT	1 cut(s)	39
BspLI	GGNNCC	2 cut(s)	579, 786
BspMAI	CTGCAG	2 cut(s)	661, 843
BspPI	GGATC	2 cut(s)	620, 644
BspQI	GCTCTTC	1 cut(s)	125
BspT107I	GGYRCC	1 cut(s)	577
BsrGI	TGTACA	2 cut(s)	327, 589
BsrI	ACTGG	2 cut(s)	187, 228
BssMI	GATC	4 cut(s)	36, 342, 625, 649
Bst2UI	CCWGG	1 cut(s)	6
Bst4CI	ACNGT	1 cut(s)	635
Bst6I	CTCTTC	1 cut(s)	125
BstAPI	GCANNNNNTGC	1 cut(s)	487
BstAUI	TGTACA	2 cut(s)	327, 589
BstC8I	GCNNGC	3 cut(s)	170, 181, 876
BstDEI	CTNAG	3 cut(s)	90, 270, 366
BstF5I	GGATG	3 cut(s)	153, 172, 592
BstKTI	GATC	4 cut(s)	39, 345, 628, 652
BstMBI	GATC	4 cut(s)	36, 342, 625, 649
BstMWI	GCNNNNNNNGC	1 cut(s)	487
BstNI	CCWGG	1 cut(s)	6
BstSCI	CCNGG	1 cut(s)	4
BstSFI	CTRYAG	2 cut(s)	657, 839
BstSLI	GKGCMC	1 cut(s)	302
BstV1I	GCAGC	5 cut(s)	444, 454, 853, 865, 868
BstV2I	GAAGAC	1 cut(s)	423
Bsu15I	ATCGAT	1 cut(s)	39
BsuRI	GGCC	2 cut(s)	201, 322
BsuTUI	ATCGAT	1 cut(s)	39
BtsCI	GGATG	3 cut(s)	153, 172, 592
BtsIMutI	CAGTG	1 cut(s)	221
Cac8I	GCNNGC	3 cut(s)	170, 181, 876
CaiI	CAGNNNCTG	1 cut(s)	719
Cfr13I	GGNCC	1 cut(s)	320
ClaI	ATCGAT	1 cut(s)	39
Csp6I	GTAC	3 cut(s)	247, 328, 590
CspCI	CAANNNNNGTGG	2 cut(s)	664, 699
CviAII	CATG	2 cut(s)	31, 541
CviJI	RGCY	8 cut(s)	118, 201, 274, 322, 370, 445, 719, 787
CviKI_1	RGCY	8 cut(s)	118, 201, 274, 322, 370, 445, 719, 787
CviQI	GTAC	3 cut(s)	247, 328, 590
DdeI	CTNAG	3 cut(s)	90, 270, 366
DpnI	GATC	4 cut(s)	38, 344, 627, 651
DpnII	GATC	4 cut(s)	36, 342, 625, 649
EaeI	YGGCCR	1 cut(s)	199
Eam1104I	CTCTTC	1 cut(s)	125
EarI	CTCTTC	1 cut(s)	125
EcoRII	CCWGG	1 cut(s)	4
FaeI	CATG	2 cut(s)	34, 544
FatI	CATG	2 cut(s)	30, 540
FauNDI	CATATG	3 cut(s)	127, 453, 558
Fnu4HI	GCNGC	5 cut(s)	443, 458, 842, 857, 879
FokI	GGATG	3 cut(s)	159, 160, 579
Fsp4HI	GCNGC	5 cut(s)	443, 458, 842, 857, 879
FspBI	CTAG	2 cut(s)	531, 886
GluI	GCNGC	5 cut(s)	443, 458, 842, 857, 879
HaeIII	GGCC	2 cut(s)	201, 322
HapII	CCGG	1 cut(s)	202
Hin1II	CATG	2 cut(s)	34, 544
HinfI	GANTC	1 cut(s)	762
HpaII	CCGG	1 cut(s)	202
Hpy166II	GTNNAC	2 cut(s)	328, 590
Hpy188I	TCNGA	3 cut(s)	271, 367, 621
Hpy188III	TCNNGA	1 cut(s)	74
Hpy8I	GTNNAC	2 cut(s)	328, 590
HpyCH4III	ACNGT	1 cut(s)	635
HpyCH4IV	ACGT	2 cut(s)	740, 870
HpyF10VI	GCNNNNNNNGC	1 cut(s)	487
HpyF3I	CTNAG	3 cut(s)	90, 270, 366
HpySE526I	ACGT	2 cut(s)	740, 870
Hsp92II	CATG	2 cut(s)	34, 544
Kzo9I	GATC	4 cut(s)	36, 342, 625, 649
LguI	GCTCTTC	1 cut(s)	125
LmnI	GCTCC	2 cut(s)	439, 784
LpnPI	CCDG	9 cut(s)	18, 87, 189, 200, 209, 215, 336, 450, 588
Lsp1109I	GCAGC	5 cut(s)	444, 454, 853, 865, 868
LweI	GCATC	2 cut(s)	181, 468
MaeI	CTAG	2 cut(s)	531, 886
MaeII	ACGT	2 cut(s)	740, 870
MaeIII	GTNAC	1 cut(s)	741
MalI	GATC	4 cut(s)	38, 344, 627, 651
MboI	GATC	4 cut(s)	36, 342, 625, 649
MboII	GAAGA	5 cut(s)	112, 428, 487, 698, 757
MhlI	GDGCHC	1 cut(s)	302
MluCI	AATT	2 cut(s)	102, 280
MmeI	TCCRAC	1 cut(s)	689
MnlI	CCTC	8 cut(s)	124, 412, 496, 538, 634, 694, 709, 802
MseI	TTAA	5 cut(s)	84, 141, 423, 572, 693
MspA1I	CMGCKG	1 cut(s)	445
MspI	CCGG	1 cut(s)	202
MspR9I	CCNGG	1 cut(s)	6
Mva1269I	GAATGC	1 cut(s)	70
MvaI	CCWGG	1 cut(s)	6
MwoI	GCNNNNNNNGC	1 cut(s)	487
NdeI	CATATG	3 cut(s)	127, 453, 558
NdeII	GATC	4 cut(s)	36, 342, 625, 649
NlaIII	CATG	2 cut(s)	34, 544
NlaIV	GGNNCC	2 cut(s)	579, 786
NmuCI	GTSAC	1 cut(s)	741
PciSI	GCTCTTC	1 cut(s)	125
PctI	GAATGC	1 cut(s)	70
PfeI	GAWTC	1 cut(s)	762
PkrI	GCNGC	5 cut(s)	444, 459, 843, 858, 880
PshBI	ATTAAT	1 cut(s)	423
Psp6I	CCWGG	1 cut(s)	4
PspGI	CCWGG	1 cut(s)	4
PspN4I	GGNNCC	2 cut(s)	579, 786
PspPI	GGNCC	1 cut(s)	320
PstI	CTGCAG	2 cut(s)	661, 843
PstNI	CAGNNNCTG	1 cut(s)	719
PvuII	CAGCTG	1 cut(s)	445
RsaI	GTAC	3 cut(s)	248, 329, 591
RsaNI	GTAC	3 cut(s)	247, 328, 590
SapI	GCTCTTC	1 cut(s)	125
SaqAI	TTAA	5 cut(s)	84, 141, 423, 572, 693
SatI	GCNGC	5 cut(s)	443, 458, 842, 857, 879
Sau3AI	GATC	4 cut(s)	36, 342, 625, 649
Sau96I	GGNCC	1 cut(s)	320
ScrFI	CCNGG	1 cut(s)	6
SduI	GDGCHC	1 cut(s)	302
SfaNI	GCATC	2 cut(s)	181, 468
SfcI	CTRYAG	2 cut(s)	657, 839
Sse9I	AATT	2 cut(s)	102, 280
SsiI	CCGC	1 cut(s)	244
SspMI	CTAG	2 cut(s)	531, 886
StyD4I	CCNGG	1 cut(s)	4
TaaI	ACNGT	1 cut(s)	635
TaiI	ACGT	2 cut(s)	743, 873
TaqI	TCGA	2 cut(s)	39, 848
TasI	AATT	2 cut(s)	102, 280
TatI	WGTACW	2 cut(s)	327, 589
TfiI	GAWTC	1 cut(s)	762
Tru1I	TTAA	5 cut(s)	84, 141, 423, 572, 693
Tru9I	TTAA	5 cut(s)	84, 141, 423, 572, 693
TscAI	CASTG	1 cut(s)	228
TseFI	GTSAC	1 cut(s)	741
TseI	GCWGC	5 cut(s)	442, 457, 841, 856, 878
Tsp45I	GTSAC	1 cut(s)	741
TspDTI	ATGAA	2 cut(s)	63, 575
TspGWI	ACGGA	1 cut(s)	253
TspRI	CASTG	1 cut(s)	228
VspI	ATTAAT	1 cut(s)	423
XapI	RAATTY	2 cut(s)	102, 280
XcmI	CCANNNNNNNNNTGG	1 cut(s)	194
XspI	CTAG	2 cut(s)	531, 886

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.